Biology subjects

Stripp, S. T.

Publications and source records attributed to Stripp, S. T..

3 recordsLinked to original sources

bioRxiv2026

The -hydrogenase SoHydAB of Shewanella oneidensis - An Atypical M2(D)-type Enzyme that Drives Formate Oxidation

The gamma-proteobacterium Shewanella oneidensis harbours one [NiFe]- and one [FeFe]-hydrogenase. This paper presents the first biochemical characterisation of SoHydAB, a M2(D)-type [FeFe]-hydrogenase consisting of a small subunit featuring a twin-arginine-targeting motif (TAT) and a large subunit harbouring the active site cofactor and two accessory iron-sulfur clusters. There are three main reasons to investigate this enzyme. Firstly, S. oneidensis is a highly studied, metabolically complex, and widely utilised organism, especially in the context of wastewater treatment, CO2 conversion, and microbial fuel cells, including H2-producing systems. Advanced understanding of its hydrogen metabolism can improve biotechnological applications. Secondly, S. oneidensis has been a mainstay of hydrogenase research for decades as its enzymes HydE, F and G are the most widely studied and utilised maturases - enzymes assembling the active site cofactor of [FeFe]-hydrogenases. Lastly, while enzymes like NdHydAB from Nitratidesulfovibrio vulgaris (formerly DdHydAB, Desulfovibrio vulgaris) with high similarity to SoHydAB have been characterised extensively in the past, the metabolic context of the enzyme in Shewanella is different from Nitratidesulfovibrio. While NdHydAB receives electrons from ferredoxin, SoHydAB accepts electrons from the menaquinone pool of the outer membrane while being a soluble enzyme in the periplasm. This is facilitated by interaction with a membrane-integrated cytochrome b transcribed from the same operon. Oxidation of the menaquinone pool drives oxidation of formate toward CO2 via formate dehydrogenase. This study therefore lays the groundwork for understanding H2-dependent CO2 turnover, a new type of metabolic niche for [FeFe]-hydrogenases, while simultaneously improving our understanding of a widely used platform organism.

biochemistry↗

bioRxiv2025

Protein dynamics affect O2-stability of Group B -hydrogenase from Thermosediminibacter oceani

In the pursuit of sustainable green energy generation, [FeFe]-hydrogenases have attracted significant attention due to their ability to catalyze hydrogen production. However, the sensitivity of these enzymes to O2 is a major obstacle for their application as biocatalysts in energy conversion technologies. In the search for an O2-stable [FeFe]-hydrogenase, we identified the hydrogenase ToHydA from Thermosediminibacter oceani that belongs to the rarely characterized Group B (M2a) [FeFe]-hydrogenases. Our findings demonstrate that ToHydA exhibits remarkable O2-stability, even under prolonged O2 exposure. By characterizing site-directed mutagenesis variants, we found that the highly conserved proton-transporting cysteine protects H-cluster from O2-induced degradation by forming Hinact state. The additional cysteine residue in the TSCCCP motif of ToHydA, a feature unique to Group B (M2a) [FeFe]-hydrogenases, enhances the flexibility of that motif and facilitates the formation of the Hinact state. Moreover, ToHydA possesses unique features, including the formation of an unusual Hinact resting state that distinguishes the enzyme from other [FeFe]-hydrogenases. Our atomistic molecular dynamics simulations reveal a previously unrecognized cluster of hydrophobic residues centered around the proton-transporting cysteine-bearing loop. This structural feature appears to be a common molecular characteristic in hydrogenases that form the O2-protected Hinact state. By exploiting these molecular features of ToHydA, future research can aim to rationally design hydrogenases that combine high catalytic activity with enhanced O2 stability, to develop more efficient and durable catalysts. Table of Contents Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/643706v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@96b4aorg.highwire.dtl.DTLVardef@62f367org.highwire.dtl.DTLVardef@59f170org.highwire.dtl.DTLVardef@fa2fd7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Energy extraction from air: structural basis of atmospheric hydrogen oxidation

Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival. This recently discovered yet globally significant process regulates the composition of the atmosphere, enhances soil biodiversity, and drives primary production in certain extreme environments. Atmospheric H2 oxidation has been attributed to still uncharacterised members of the [NiFe]-hydrogenase superfamily. However, it is unresolved how these enzymes overcome the extraordinary catalytic challenge of selectively oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2, and how the derived electrons are transferred to the respiratory chain. Here we determined the 1.52 [A] resolution CryoEM structure of the mycobacterial hydrogenase Huc and investigated its mechanism by integrating kinetics, electrochemistry, spectroscopy, mass spectrometry, and molecular dynamics simulations. Purified Huc is an oxygen-insensitive enzyme that couples the oxidation of atmospheric H2 at its large subunit to the hydrogenation of the respiratory electron carrier menaquinone at its small subunit. The enzyme uses a narrow hydrophobic gas channel to selectively bind atmospheric H2 at the expense of O2, while three [3Fe-4S] clusters and their unusual ligation by a D-histidine modulate the electrochemical properties of the enzyme such that atmospheric H2 oxidation is energetically feasible. Huc forms an 833 kDa complex composed of an octamer of catalytic subunits around a membrane-associated central stalk, which extracts and transports menaquinone a remarkable 94 [A] from the membrane, enabling its reduction. These findings provide a mechanistic basis for the biogeochemically and ecologically critical process of atmospheric H2 oxidation. Through the first characterisation of a group 2 [NiFe]-hydrogenase, we also uncover a novel mode of energy coupling dependent on long-range quinone transport and pave way for the development of biocatalysts that oxidize H2 in ambient air.

biochemistry↗